We can “know” that an intelligent cause is the best explanation in precisely the same way that we infer materialistic causes.
Ironically, when critics make this accusation, they are usually committing a “gaps” fallacy themselves.
Intelligent-design theorists have long argued that finding complex and specified information (CSI) is the best way to reliably detect intelligent design in nature.
ID is a historical science based upon the principle of uniformitarianism.
Apart from the occasional mutation, we often think of the information in DNA as static, like a read-only CD-ROM.